Water quality investigations and underwater visual observations were carried out in ten fish farms located at Datça-Bozburun and Gökova specially protected areas (southern Aegean Sea, Turkey). Investigations revealed that the substrate was disturbed and species composition changed as a consequence of increased sedimentation and excessive nutrient input at the vicinity of fish farms where the current velocity was low. Two most frequently observed grazers in mediolittoral areas of the region, Patella caerulea and Osilinus turbinatus, were not detected near fish farms in Bozburun peninsula, where sessile filter-feeding cirripedes were the dominant components of the shallow water macrobenthic community. Observations conducted on two closely located fish farms in Gökova Bay depicted the importance of current velocities in structuring the ecological quality of the marine environment. Species composition changed in favor of filter feeders and detritivorous species in the surrounding area of the enclosed farm where the current velocity was less than 5 cm/sec. In conclusion, it was observed that fish farms planned without considering bathymetry and water circulation caused serious impacts such as habitat loss, changes in species composition and degradation of water quality, whereas farms constructed at well-circulated and deep regions had no significant negative impacts on marine environment.